Skip to content

Commit 08ba52b

Browse files
sblivensbliven
committed
Reformating code in genebank
1 parent dcd3b3f commit 08ba52b

File tree

1 file changed

+75
-71
lines changed

1 file changed

+75
-71
lines changed

‎genomics/genebank.md‎

Lines changed: 75 additions & 71 deletions
Original file line numberDiff line numberDiff line change
@@ -6,67 +6,71 @@ There are multiple ways how to read a Genbank file.
66
## Method 1: Read a Genbank file using the GenbankProxySequenceReader
77

88
```java
9-
10-
GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
11-
= new GenbankProxySequenceReader<AminoAcidCompound>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
12-
ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
13-
genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
14-
System.out.println("Sequence" + "(" + proteinSequence.getAccession() + "," + proteinSequence.getLength() + ")=" +
15-
proteinSequence.getSequenceAsString().substring(0, 10) + "...");
16-
17-
GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
18-
= new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
19-
DNASequence dnaSequence = new DNASequence(genbankDNAReader);
20-
genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
21-
System.out.println("Sequence" + "(" + dnaSequence.getAccession() + "," + dnaSequence.getLength() + ")=" +
22-
dnaSequence.getSequenceAsString().substring(0, 10) + "...");
23-
9+
GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader =
10+
new GenbankProxySequenceReader<AminoAcidCompound>("/tmp", "NP_000257",
11+
AminoAcidCompoundSet.getAminoAcidCompoundSet());
12+
ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
13+
genbankProteinReader.getHeaderParser().parseHeader(
14+
genbankProteinReader.getHeader(), proteinSequence);
15+
System.out.format("Sequence(%s,%d)=%s...",
16+
proteinSequence.getAccession(),
17+
proteinSequence.getLength(),
18+
proteinSequence.getSequenceAsString().substring(0, 10));
19+
20+
GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader =
21+
new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126",
22+
DNACompoundSet.getDNACompoundSet());
23+
DNASequence dnaSequence = new DNASequence(genbankDNAReader);
24+
genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
25+
System.out.format("Sequence(%s,%d)=%s...", dnaSequence.getAccession(),
26+
dnaSequence.getLength(),
27+
dnaSequence.getSequenceAsString().substring(0, 10));
2428
```
2529

2630

2731
## Method 2: Read a Genbank file using GenbankReaderHelper
2832

2933
```java
30-
File dnaFile = new File("src/test/resources/NM_000266.gb");
31-
File protFile = new File("src/test/resources/BondFeature.gb");
32-
33-
LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence( dnaFile );
34-
for (DNASequence sequence : dnaSequences.values()) {
35-
System.out.println( sequence.getSequenceAsString() );
36-
}
37-
38-
LinkedHashMap<String, ProteinSequence> protSequences = GenbankReaderHelper.readGenbankProteinSequence(protFile);
39-
for (ProteinSequence sequence : protSequences.values()) {
40-
System.out.println( sequence.getSequenceAsString() );
41-
}
42-
34+
File dnaFile = new File("src/test/resources/NM_000266.gb");
35+
File protFile = new File("src/test/resources/BondFeature.gb");
36+
37+
LinkedHashMap<String, DNASequence> dnaSequences =
38+
GenbankReaderHelper.readGenbankDNASequence( dnaFile );
39+
for (DNASequence sequence : dnaSequences.values()) {
40+
System.out.println( sequence.getSequenceAsString() );
41+
}
42+
43+
LinkedHashMap<String, ProteinSequence> protSequences =
44+
GenbankReaderHelper.readGenbankProteinSequence(protFile);
45+
for (ProteinSequence sequence : protSequences.values()) {
46+
System.out.println( sequence.getSequenceAsString() );
4347
```
4448

4549
## Method 3: Read a Genbank file using the GenbankReader Object
4650

4751
```java
48-
49-
FileInputStream is = new FileInputStream(dnaFile);
50-
GenbankReader<DNASequence, NucleotideCompound> dnaReader = new GenbankReader<DNASequence, NucleotideCompound>(
51-
is,
52-
new GenericGenbankHeaderParser<DNASequence,NucleotideCompound>(),
53-
new DNASequenceCreator(DNACompoundSet.getDNACompoundSet())
54-
);
55-
dnaSequences = dnaReader.process();
56-
is.close();
57-
System.out.println(dnaSequences);
58-
59-
is = new FileInputStream(protFile);
60-
GenbankReader<ProteinSequence, AminoAcidCompound> protReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
61-
is,
62-
new GenericGenbankHeaderParser<ProteinSequence,AminoAcidCompound>(),
63-
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())
64-
);
65-
protSequences = protReader.process();
66-
is.close();
67-
System.out.println(protSequences);
68-
69-
```
52+
FileInputStream is = new FileInputStream(dnaFile);
53+
GenbankReader<DNASequence, NucleotideCompound> dnaReader =
54+
new GenbankReader<DNASequence, NucleotideCompound>(
55+
is,
56+
new GenericGenbankHeaderParser<DNASequence,NucleotideCompound>(),
57+
new DNASequenceCreator(DNACompoundSet.getDNACompoundSet())
58+
);
59+
dnaSequences = dnaReader.process();
60+
is.close();
61+
System.out.println(dnaSequences);
62+
63+
is = new FileInputStream(protFile);
64+
GenbankReader<ProteinSequence, AminoAcidCompound> protReader =
65+
new GenbankReader<ProteinSequence, AminoAcidCompound>(
66+
is,
67+
new GenericGenbankHeaderParser<ProteinSequence,AminoAcidCompound>(),
68+
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())
69+
);
70+
protSequences = protReader.process();
71+
is.close();
72+
System.out.println(protSequences);
73+
```
7074

7175

7276
# Write a Genbank file
@@ -75,28 +79,28 @@ dnaSequence.getSequenceAsString().substring(0, 10) + "...");
7579
Use the GenbankWriterHelper to write DNA sequences into a Genbank file.
7680

7781
```java
78-
79-
// First let's read dome DNA sequences from a genbank file
80-
81-
File dnaFile = new File("src/test/resources/NM_000266.gb");
82-
LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence( dnaFile );
83-
ByteArrayOutputStream fragwriter = new ByteArrayOutputStream();
84-
ArrayList<DNASequence> seqs = new ArrayList<DNASequence>();
85-
for(DNASequence seq : dnaSequences.values()) {
86-
seqs.add(seq);
87-
}
88-
89-
// ok now we got some DNA sequence data. Next step is to write it
90-
91-
GenbankWriterHelper.writeNucleotideSequence(fragwriter, seqs,
92-
GenbankWriterHelper.LINEAR_DNA);
93-
94-
// the fragwriter object now contains a string representation in the Genbank format
95-
// and you could write this into a file
96-
// or print it out on the console
97-
System.out.println(fragwriter.toString());
98-
82+
// First let's read dome DNA sequences from a genbank file
83+
84+
File dnaFile = new File("src/test/resources/NM_000266.gb");
85+
LinkedHashMap<String, DNASequence> dnaSequences =
86+
GenbankReaderHelper.readGenbankDNASequence( dnaFile );
87+
ByteArrayOutputStream fragwriter = new ByteArrayOutputStream();
88+
ArrayList<DNASequence> seqs = new ArrayList<DNASequence>();
89+
for(DNASequence seq : dnaSequences.values()) {
90+
seqs.add(seq);
91+
}
92+
93+
// ok now we got some DNA sequence data. Next step is to write it
94+
95+
GenbankWriterHelper.writeNucleotideSequence(fragwriter, seqs,
96+
GenbankWriterHelper.LINEAR_DNA);
97+
98+
// the fragwriter object now contains a string representation in the Genbank format
99+
// and you could write this into a file
100+
// or print it out on the console
101+
System.out.println(fragwriter.toString());
99102
```
103+
100104
<!--automatically generated footer-->
101105

102106
---

0 commit comments

Comments
 (0)